St. Thomas the Apostle School is committed to the essential sacramental needs of its students, faculty and staff with a weekly, all-school celebration of the Holy Sacrifice of the Mass and, at least monthly, opportunities for the Sacrament of Confession. In addition to the weekly Mass for the whole school, the Mass is celebrated together for Holy Days of Obligation and for other liturgical celebrations like the May Crowning of Our Lady.

Beyond the regular reception of the Sacraments mentioned, St. Thomas has a comprehensive sacramental preparation program for students in 2nd Grade, to prepare students for their first Confession and their First Holy Communion as well as for 8th grade students to prepare them for the Sacrament of Confirmation. Preparation for Confirmation continues into high school through the Youth Ministry of St. Thomas Parish.